mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-01 15:37:32 +08:00
Dannon Baker
83 lines
4.1 KiB
XML
83 lines
4.1 KiB
XML
<tool id="interactive_tool_askomics" tool_type="interactive" name="AskOmics" version="4.3.1">
|
|
<icon src="askomics.png" />
|
|
<description>a visual SPARQL query builder</description>
|
|
<requirements>
|
|
<container type="docker">askomics/flaskomics-with-dependencies:4.3.1</container>
|
|
</requirements>
|
|
<entry_points>
|
|
<entry_point name="AskOmics instance" requires_domain="True">
|
|
<port>5000</port>
|
|
<url>/loginapikey/${__user_name__}</url>
|
|
</entry_point>
|
|
</entry_points>
|
|
<environment_variables>
|
|
<!-- AskOmics user -->
|
|
<environment_variable name="CREATE_USER">true</environment_variable>
|
|
<environment_variable name="USER_FIRST_NAME">${__user_name__}</environment_variable>
|
|
<environment_variable name="USER_LAST_NAME">Galaxy</environment_variable>
|
|
<environment_variable name="USER_USERNAME">${__user_name__}</environment_variable>
|
|
<environment_variable name="USER_EMAIL">${__user_email__}</environment_variable>
|
|
<environment_variable name="USER_APIKEY">${__user_name__}</environment_variable>
|
|
<!-- Galaxy info -->
|
|
<environment_variable name="GALAXY_URL">$__galaxy_url__</environment_variable>
|
|
<environment_variable name="GALAXY_API_KEY" inject="api_key" />
|
|
<!-- AskOmics config -->
|
|
<environment_variable name="DEPMODE">prod</environment_variable>
|
|
<environment_variable name="MAX_CELERY_QUEUE">10</environment_variable>
|
|
<environment_variable name="ASKO_askomics_subtitle">Galaxy</environment_variable>
|
|
<environment_variable name="ASKO_askomics_footer_message">AskOmics Interactive Tool for Galaxy</environment_variable>
|
|
<environment_variable name="ASKO_askomics_data_directory">/tmp/askomics-it</environment_variable>
|
|
<environment_variable name="ASKO_askomics_database_path">/tmp/askomics-it/database.db</environment_variable>
|
|
<environment_variable name="ASKO_triplestore_load_url">http://localhost:5000</environment_variable>
|
|
<!-- Virtuoso config -->
|
|
<environment_variable name="SPARQL_UPDATE">true</environment_variable>
|
|
<!--
|
|
Update the following environment variables according to how much memory you want to allow to virtuoso
|
|
see https://github.com/askomics/flaskomics-docker-compose#configure-virtuoso for help
|
|
-->
|
|
<environment_variable name="VIRT_Parameters_NumberOfBuffers">170000</environment_variable>
|
|
<environment_variable name="VIRT_Parameters_MaxDirtyBuffers">130000</environment_variable>
|
|
<!-- Corese config -->
|
|
<environment_variable name="MEM">2G</environment_variable>
|
|
</environment_variables>
|
|
<command><![CDATA[
|
|
#import re
|
|
|
|
cd /askomics &&
|
|
source /askomics/venv/bin/activate &&
|
|
mkdir -p /import &&
|
|
|
|
#if $infiles:
|
|
#for $input in $infiles:
|
|
#set link_name = re.sub('[^\w\-\.]', '_', str($input.element_identifier))
|
|
#if $input.ext == 'tabular':
|
|
#set link_name = $link_name
|
|
#elif $input.ext == 'interval':
|
|
#set link_name = $link_name + '.bed'
|
|
#else:
|
|
#set link_name = $link_name + '.' + $input.ext
|
|
#end if
|
|
ln -s '$input' '/import/$link_name' &&
|
|
#end for
|
|
#end if
|
|
|
|
bash /askomics/cli/set_config.sh &&
|
|
bash /askomics/cli/set_user.sh &&
|
|
python3 /askomics/cli/upload_files.py -c /askomics/config/askomics.ini -d /import -k $__user_name__ &&
|
|
bash /askomics/docker/start_all.sh
|
|
]]>
|
|
</command>
|
|
<inputs>
|
|
<param name="infiles" type="data" optional="true" multiple="true" format="tabular,gff,gff3,interval,xml,ttl,nt" label="Datasets to load into AskOmics"/>
|
|
</inputs>
|
|
<outputs>
|
|
<data name="outfile" format="txt" />
|
|
</outputs>
|
|
<tests>
|
|
</tests>
|
|
<help>
|
|
AskOmics is a visual SPARQL query interface supporting both intuitive data integration and
|
|
querying while shielding the user from most of the technical difficulties underlying RDF and SPARQL.
|
|
</help>
|
|
</tool>
|